Proteomic Profiling Assessed by Data-Independent Acquisition Mass Spectrometry Revealed Enrichment in Myofibrillogenesis in the Heart Primordium after Heartbeat Initiation in Rats.
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus Rattus (black Rat)
SUBMITTER: Tatsuya Sato
PROVIDER: PXD032987 | JPOST Repository | Thu Jun 02 00:00:00 BST 2022
REPOSITORIES: jPOST
Publications
Ultrastructural Assessment and Proteomic Analysis in Myofibrillogenesis in the Heart Primordium After Heartbeat Initiation in Rats.
Ichise Nobutoshi N Sato Tatsuya T Fusagawa Hiroyori H Yamazaki Hiroya H Kudo Taiki T Ogon Izaya I Tohse Noritsugu N
Frontiers in physiology 20220509
Myofibrillogenesis is an essential process for cardiogenesis and is closely related to excitation-contraction coupling and the maintenance of heartbeat. It remains unclear whether the formation of myofibrils and sarcomeres is associated with heartbeat initiation in the early embryonic heart development. Here, we investigated the association between the ultrastructure of myofibrils assessed by transmission electron microscopy and their proteomic profiling assessed by data-independent acquisition ...[more]
Similar Datasets
Project description:The initiation of heartbeat is an essential step in cardiogenesis in the heart primordium, but it remains unclear how intracellular metabolism responds to increased energy demands after heartbeat initiation. In this study, embryos in Wistar rats at embryonic day 10, at which heartbeat begins in rats, were divided into two groups by the heart primordium before and after heartbeat initiation and their metabolic characteristics were assessed. Metabolome analysis revealed that increased levels of ATP, a main product of glucose catabolism, and reduced glutathione, a by-product of the pentose phosphate pathway, were the major determinants in the heart primordium after heartbeat initiation. Glycolytic capacity and ATP synthesis-linked mitochondrial respiration were significantly increased, but subunits in complexes of mitochondrial oxidative phosphorylation were not upregulated in the heart primordium after heartbeat initiation. Hypoxia-inducible factor (HIF)-1α was activated and a glucose transporter and rate-limiting enzymes of the glycolytic and pentose phosphate pathways, which are HIF-1α-downstream targets, were upregulated in the heart primordium after heartbeat initiation. These results suggest that the HIF-1α-mediated enhancement of glycolysis with activation of the pentose phosphate pathway, potentially leading to antioxidant defense and nucleotide biosynthesis, covers the increased energy demand in the beating and developing heart primordium.
2021-10-14 | GSE185702 | GEO
Project description:We aimed to identify gene variants associated with heart failure by using a rat model of the human disease. We performed invasive cardiac hemodynamic measurements in F2 crosses between spontaneously hypertensive heart failure rats (SHHF) and reference strains. We combined linkage analyses with genome-wide expression profiling .
2008-09-01 | E-TABM-418 | biostudies-arrayexpress
Project description:We have generated scRNA-seq data from embryonic day (E)10.5 and E12.5 atrioventricular canals (primitive heart valves) to assess cellular diversity during the distinct epithelial-to-mesenchymal transitions (EMTs) from endocardium and epicardium that guide the formation of valve mesenchyme. Alongside, wildtype atrioventricular canals, we generated scRNA-seq data from Sox9 conditional knockouts (Sox9fl/fl;Tie2-cre) to explore the role of SOX9 in EMT. Atrioventricular canals were microdissected from cardiac chambers and outflow tract, enriching for heart valve progenitor lineages.
2023-06-30 | E-MTAB-11795 | biostudies-arrayexpress
Project description:Specific gene changes after exposure to the heart toxin, bis(2-chloroethoxy)methane, were analyzed to elucidate critical pathways associated with recovery from heart toxicity. Bis(2-chloroethoxy)methane was administered to male F344/N rats at 0, 200, 400, or 600 mg/kg by dermal exposure for up to 16 days. Heart toxicity occurred at day 2 of exposure in all three regions of the heart (atrium, ventricle, interventricular septum) and was characterized by myofiber vacuolation, necrosis, mononuclear-cell infiltration, and atrial thrombosis. Ultrastructural analysis revealed that the primary site of damage occured in the mitochondrion. Damaged mitochondria had disrupted cristae and loss of membrane structure, and distention of the myocardial sarcoplasmic reticulum. By day 5, even though daily dosing was continued, the heart toxic lesions begin to resolved. By day 16, even though BCEM treatment continued, the heart appeared normal. RNA was extracted from control and dosed rats at day 2 and day 5, and analyzed for gene change by PCR. Gene changes associated with promoting cell growth including up regulation of growth factors and cell adhesion molecules were up regulated. Temperature regulation was promoted by up regulation of uncoupling proteins. Genes controlling the action potential of the heart, including ion flow and G protein signals, were altered. Because mitochondria are damaged by BCEM exposure, preserving and restoring energy function to the heart is considered to be essential, and up regulation of components of the ATP synthase unit occurred by day 5. Significant gene changes included up regulation of transcription factors, growth factors, membrane bound G protein signals, and ion transport controls. Multiple gene changes in the heart may contribute to restoration of heart function after exposure to environmental cardiotoxins. Experiment Overall Design: Chemical and Animal exposures: Experiment Overall Design: Bis(2-chloroethoxy)methane (CAS No. 11-91-1; lot B004160277) (Karl Industries, Aurora, OH) (Fig, 1) was found to be 98.5% pure (Dunnick et al. 2004a; Dunnick et al. 2004b) . Solutions of BCEM were prepared in 95% ethanol for dosing by dermal administration daily to male F344 rats, excluding weekends, for two weeks plus two consecutive dosages before the last sacrifice on study-day 16, at which animals had received a total of 12 doses. Fur from the site of application was clipped weekly. Stock solutions prepared at concentrations of 0, 800, and 1200 mg/ml were stored in amber glass bottles at room temperature. The administrations were applied to the skin of the male rats at 0.5 ml/kg body to deliver doses of 0, 400, or 600 mg/kg body weight. All dose formulations were determined to be within ï±10% of target concentrations. Approximately 45% of a dermal dose of CEM is adsorbed (NIEHS Contract NO1-ES-75407 2002). Male F344/N rats (Taconic Laboratories, Germantown, NY) were placed on study at 5 weeks of age and housed one per cage in polycarbonate cages in rooms maintained at temperatures between 69 and 75ï°F with 35 â 65% relative humidity and a 12-hr light/dark cycle. Control and treated groups received irradiated NTP-2000 diet (Zeigler Brothers, Gardners, PA) ad libitum. Experiment Overall Design: Histopathology: Experiment Overall Design: Animals were anesthetized with CO 2 and heart collected and preserved in 10% formalin. Slides were made from paraffin sections from rats treated with BCEM as previously described (Dunnick et al. 2004a). Pathologic analysis included comparing heart lesions in male rats after 2, 3, 5, and 16 days of treatment. Experiment Overall Design: RNA Extraction Methods Experiment Overall Design: RNA was extracted from hearts of three control animal at day 2, three control rats at day 5, three rats exposed to 200, 400, or 600 mg/kg BCEM at day 2 and three at day 5. Animals designated for heart RNA extraction were anesthetized with CO2/O2 on study days 2 and 5, exanguinated, and their hearts infused with RNAlater. Total cardiac RNA was isolated from hearts using the QIAGEN Rneasy kit (QIAGEN, Valencia, CA). The RNA was quantified through optical density measurements and agarose gel electrophoresis, and kept frozen at â 70 C. RNA was extracted from control, 200, 400, and 600 mg/kg rats.
2008-06-13 | E-GEOD-4254 | biostudies-arrayexpress
Project description:Left heart disease (LHD) frequently causes lung vascular remodelling and pulmonary hypertension (PH). Yet, pharmacological treatment for PH in LHD is lacking and its pathophysiological basis remains obscure. We aimed to identify candidate mechanisms of PH in LHD and to test their relevance and therapeutic potential. In rats, LHD was induced by supracoronary aortic banding. Whole genome microarray analyses were performed, candidate genes were confirmed by RT-PCR and Western blots and functional relevance was tested in vivo by genetic and pharmacological strategies. In lungs of LHD rats, mast cell activation was the most prominently upregulated gene ontology cluster. Mast cell gene upregulation was confirmed at RNA and protein levels and remodelled vessels showed perivascular mast cell accumulations. In LHD rats treated with the mast cell stabiliser ketotifen, or in mast cell deficient Ws/Ws rats, PH and vascular remodelling were largely attenuated. Both strategies also reduced PH and vascular remodelling in monocrotaline-induced pulmonary arterial hypertension, suggesting that the role of mast cells extends to noncardiogenic PH. In PH of different aetiologies, mast cells accumulate around pulmonary blood vessels and contribute to vascular remodelling and PH. Mast cells and mast cell-derived mediators may present promising targets for the treatment of PH. Whole rat genome microarray analyses were performed in lung homogenates of three rats with established PH following supracoronary aortic banding and in three sham-operated controls. Out of a total of 28,000 analysed genes, differential expression defined as 2-fold change with p<0.05 was evident for 120 genes. Of these, 76 were upregulated and 44 downregulated in aortic banding compared with control lungs gene. Enrichment analysis revealed regulation of mast cell specific genes - 13 out of 20 genes were significantly upregulated in aortic banding compared with control lungs. To test for a putative functional role of mast cells in lung vascular remodelling and PH in LHD, we applied a pharmacological approach by treatment of aortic banding rats with the mast cell stabiliser ketotifen. Microarray analysis then compared rats that were treated with untreated. In brief, congestive heart failure (CHF) was induced in juvenile rats by supracoronary aortic banding and rats were analyzed 9 weeks thereafter when they had established left heart failure with preserved ejection fraction and secondary pulmonary hypertension. Three heart failure rats were untreated, and 3 received the mast cell stabilizer ketotifen (1 mg/kg-1 bodyweight/day-1) with the drinking water. Sham rats underwent the same surgical procedure but without placement of a clip on the supracoronary aorta. Microarray analyses: Lungs from banded and control rats were excised and total RNA was extracted (Stratagene Absolutely RNA Miniprep Kit; Stratagene, La Jolla, USA). Three µg total RNA from three control and three banded rats each were processed according to the One-Cycle Target Labeling protocol (GeneChip Expression Analysis, Affymetrix, Santa Clara, USA). Before and after amplifications, the total RNA/complementary RNA concentrations were checked with NanoDrop ND-1000 (Thermo Scientific, Wilmington, USA) and quality was controlled (Experion electrophoresis station, BioRad; Hercules, USA). Samples were hybridized to GeneChip® Rat Genome 230 2.0 arrays (Affymetrix; Santa Clara, USA) containing 31,000 probe sets covering 28,000 rat genes.
2016-07-22 | E-GEOD-84704 | biostudies-arrayexpress
Project description:The molecular mechanisms governing heart development provide an important framework to understand congenital heart disease. The embryonic vertebrate heart tube develops an atrioventricular canal that divides the atrial and ventricular chambers, forms atrioventricular conduction tissue and organizes valve development. To better understand the molecular mechanism underlying atrioventricular canal versus chamber myocardium expression, a double-reporter transgenic mouse line was generated in which the expression of EGFP (green fluorescent protein) and Katushka (red fluorescent protein) are selectively expressed in the atrioventricular canal and in the chamber myocardium, respectively. We assessed the genome-wide H3K27ac pattern in isolated embryonic AV canal and in chamber cardiomyocytes, respectively.
2014-03-06 | GSE55611 | GEO
Project description:Male Sprague-Dawley (SD) rats (350 - 400 g) were anaesthetized with 3% isoflurane for 3 min in a closed induction chamber. A helium driven shock tube was used at various shock wave pressures (20 - 30 psi). The exposure system has been developed so that the animals are exposed head only to a ?primary blast? that being a single pulse shock wave with only minimal concussive and whiplash effects. After exposure, rats were closely observed for either 1 day or 7 days before being sacrificed. At the end of the observation period, rat whiskers were quickly pulled and placed in a 1.5 ml micro centrifuge tube containing 0.5 ml of RNAlater. Samples were then stored at -80C until further analysis.
2014-04-01 | GSE46367 | GEO
Project description:Specific gene changes after exposure to the heart toxin, bis(2-chloroethoxy)methane, were analyzed to elucidate critical pathways associated with recovery from heart toxicity. Bis(2-chloroethoxy)methane was administered to male F344/N rats at 0, 200, 400, or 600 mg/kg by dermal exposure for up to 16 days. Heart toxicity occurred at day 2 of exposure in all three regions of the heart (atrium, ventricle, interventricular septum) and was characterized by myofiber vacuolation, necrosis, mononuclear-cell infiltration, and atrial thrombosis. Ultrastructural analysis revealed that the primary site of damage occured in the mitochondrion. Damaged mitochondria had disrupted cristae and loss of membrane structure, and distention of the myocardial sarcoplasmic reticulum. By day 5, even though daily dosing was continued, the heart toxic lesions begin to resolved. By day 16, even though BCEM treatment continued, the heart appeared normal. RNA was extracted from control and dosed rats at day 2 and day 5, and analyzed for gene change by PCR. Gene changes associated with promoting cell growth including up regulation of growth factors and cell adhesion molecules were up regulated. Temperature regulation was promoted by up regulation of uncoupling proteins. Genes controlling the action potential of the heart, including ion flow and G protein signals, were altered. Because mitochondria are damaged by BCEM exposure, preserving and restoring energy function to the heart is considered to be essential, and up regulation of components of the ATP synthase unit occurred by day 5. Significant gene changes included up regulation of transcription factors, growth factors, membrane bound G protein signals, and ion transport controls. Multiple gene changes in the heart may contribute to restoration of heart function after exposure to environmental cardiotoxins. Keywords: toxicity, recovery, cardiac, heart
2006-12-31 | GSE4254 | GEO
Project description:Single-cell RNA sequencing was performed on embryonic Drosophila heart cells. Analysis of single-cell RNA sequence (scRNA-seq) data at timepoints prior to migration of cardiac progenitor cells through to heart tube closure (embryonic stages 13, 14-early, 14-late, 15 and 16) revealed several interesting findings. We found specification of cardiac cell types takes place early, before stage 13, with biggest changes in transcriptomic profiles detected once cells had settled at the midline for further cardioblast maturation. Throughout development, our data identified multiple cell types, covering cardioblasts and five types of pericardial cells including a neural cardiac cell type. The scRNA-seq data further revealed a combination of first and second heart fields during heart development in fly. Further, we uncovered new cell type-specific markers discerning the different cardiac cell types. And we identified signaling pathways key to heart cell maturation, which are conserved from fly to human.
2023-08-07 | GSE168774 | GEO
Project description:Objective: To evaluate the altered expression of genes due to hyperglycaemia during foetal development in heart. Methods: To understand the molecular defects in the two-days old neonatal rats, diabetic female rats were bred with healthy male rats and collected two days old hearts from neonates. Heart mRNA profiles of two-day-old neonatal rats were generated by RNA sequencing, in quadruplicate, using Illumina HiSeq. Results: Using an optimized data analysis workflow, we mapped about 27 million sequence reads per sample to the rat genome (build Rnor_6.0) and identified 25456 transcripts in the heart of the neonatal rats. Approximately 4% of the transcripts showed differential expression between the Control and PGDM (pregestational diabetes mellitus) heart, with a fold change ≥2 and p value <0.05. Conclusions: Transcriptomic profiling of the RNA-seq data revealed that several of the altered genes were associated with cardiac pathogenesis in neonatal heart during PGDM.
2022-07-01 | GSE196242 | GEO